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Merge pull request #25 from TheJacksonLaboratory/task/add-search-db-m…
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…igrations-sql

Adding search sql migration files
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@bergsalex
bergsalex authored Sep 25, 2024
2 parents 43420f8 + 734325d commit bb56167
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14 changes: 14 additions & 0 deletions migration/115-create-view-geneset2hom.sql
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CREATE MATERIALIZED VIEW extsrc.geneset2hom AS
SELECT g.gs_id, array_agg(h.hom_id) as hom_id_array
FROM extsrc.homology h
INNER JOIN extsrc.geneset_value gv ON
h.ode_gene_id = gv.ode_gene_id
INNER JOIN production.geneset g ON gv.gs_id = g.gs_id
WHERE g.gs_status NOT LIKE 'de%'
AND hom_id IN
(SELECT DISTINCT hom_id
FROM extsrc.homology)
GROUP BY g.gs_id;

CREATE INDEX geneset2hom_gs_id_index
ON extsrc.geneset2hom (gs_id);
179 changes: 179 additions & 0 deletions migration/116-geneset-and-publication-full-text-search.sql
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------------------------------------------------------------------------------------------------------------------------
-- GeneSets Table Search
------------------------------------------------------------------------------------------------------------------------

-- GeneSets: Alter Table
ALTER TABLE production.geneset
ADD COLUMN gs_tsvector tsvector;

-- GeneSets: Initial tsvector creation
UPDATE geneset
SET gs_tsvector = setweight(to_tsvector('english', coalesce(gs_name, '')), 'A') ||
setweight(to_tsvector('english', coalesce(gs_description, '')), 'B') ||
setweight(to_tsvector('english', coalesce(gs_abbreviation, '')), 'C')
WHERE gs_tsvector IS NULL;

-- GeneSets: Create index on tsvector
CREATE INDEX geneset_fts_idx ON geneset USING gin (gs_tsvector);

-- GeneSets: Create update function
CREATE OR REPLACE FUNCTION geneset_tsvector_update() RETURNS trigger AS $$
BEGIN
NEW.gs_tsvector := setweight(to_tsvector('english', coalesce(NEW.gs_name, '')), 'A') ||
setweight(to_tsvector('english', coalesce(NEW.gs_description, '')), 'B') ||
setweight(to_tsvector('english', coalesce(NEW.gs_abbreviation, '')), 'C');
RETURN NEW;
END;
$$ LANGUAGE plpgsql;

-- GeneSets: Create update trigger
CREATE TRIGGER update_geneset_tsvector BEFORE INSERT OR UPDATE
ON geneset
FOR EACH ROW EXECUTE FUNCTION geneset_tsvector_update();


------------------------------------------------------------------------------------------------------------------------
-- Publication Table Search
------------------------------------------------------------------------------------------------------------------------
-- Publication: Alter Table
ALTER TABLE production.publication
ADD COLUMN pub_tsvector tsvector;

-- Publication: Initial tsvector creation
UPDATE publication
SET pub_tsvector = setweight(to_tsvector('english', coalesce(pub_title, '')), 'A') ||
setweight(to_tsvector('english', coalesce(pub_pubmed, '')), 'A') ||
setweight(to_tsvector('english', coalesce(pub_authors, '')), 'B') ||
setweight(to_tsvector('english', coalesce(pub_abstract, '')), 'C') ||
setweight(to_tsvector('english', coalesce(pub_journal, '')), 'D');

-- Publication: Create index on tsvector
CREATE INDEX publication_fts_idx ON publication USING gin(pub_tsvector);

-- Publication: Create update function
CREATE OR REPLACE FUNCTION publication_tsvector_update() RETURNS trigger AS $$
BEGIN
NEW.pub_tsvector := setweight(to_tsvector('english', coalesce(NEW.pub_title, '')), 'A') ||
setweight(to_tsvector('english', coalesce(NEW.pub_pubmed, '')), 'A') ||
setweight(to_tsvector('english', coalesce(NEW.pub_authors, '')), 'B') ||
setweight(to_tsvector('english', coalesce(NEW.pub_abstract, '')), 'C') ||
setweight(to_tsvector('english', coalesce(NEW.pub_journal, '')), 'D');
RETURN NEW;
END;
$$ LANGUAGE plpgsql;

-- Publication: Create update trigger
CREATE TRIGGER publication_tsvector_update BEFORE INSERT OR UPDATE
ON publication
FOR EACH ROW EXECUTE FUNCTION publication_tsvector_update();


------------------------------------------------------------------------------------------------------------------------
-- GeneSet Comprehensive Search
------------------------------------------------------------------------------------------------------------------------
CREATE MATERIALIZED VIEW production.geneset_search AS
WITH geneset_query AS (
SELECT gs.gs_id, 'GS'||gs.gs_id AS gsid_prefixed,
gs.gs_name AS name,
gs.gs_description AS description,
gs.gs_abbreviation AS label,
gs.usr_id,
gs.gs_count,
gs.gs_threshold_type,
gs.gs_gene_id_type,
p.pub_id,
p.pub_pubmed,
p.pub_authors,
p.pub_title,
p.pub_abstract,
p.pub_journal,
sp.sp_name AS species,
sp.sp_taxid AS taxid,
COALESCE(gs.cur_id, 0) AS cur_id,
COALESCE(gs.sp_id, 0) AS sp_id,
COALESCE(gs.gs_attribution, 0) AS attribution,
CASE
WHEN gs.gs_status='provisional' THEN 1
WHEN gs.gs_status LIKE 'deprecated%' THEN 2
ELSE 0
END AS gs_status,
CASE
WHEN gs.sp_id=1 THEN 'mouse'
WHEN gs.sp_id=2 THEN 'human'
WHEN gs.sp_id=3 THEN 'rat'
WHEN gs.sp_id=4 THEN 'zebrafish'
WHEN gs.sp_id=5 THEN 'fly'
WHEN gs.sp_id=6 THEN 'monkey'
WHEN gs.sp_id=8 THEN 'c. elegans'
WHEN gs.sp_id=9 THEN 'yeast'
END AS common_name,
CASE
WHEN gs.gs_threshold_type=1 THEN 'p-value'
WHEN gs.gs_threshold_type=2 THEN 'q-value'
WHEN gs.gs_threshold_type=3 THEN 'binary'
WHEN gs.gs_threshold_type=4 THEN 'correlation'
WHEN gs.gs_threshold_type=5 THEN 'effect'
END AS threshold_name,
CASE
WHEN gs.gs_threshold_type=-1 THEN 'Entrez'
WHEN gs.gs_threshold_type=-2 THEN 'Ensemble Gene'
WHEN gs.gs_threshold_type=-3 THEN 'Ensemble Protein'
WHEN gs.gs_threshold_type=-4 THEN 'Ensemble Transcript'
WHEN gs.gs_threshold_type=-5 THEN 'Unigene'
WHEN gs.gs_threshold_type=-7 THEN 'Gene Symbol'
WHEN gs.gs_threshold_type=-8 THEN 'Unannotated'
WHEN gs.gs_threshold_type=-10 THEN 'MGI'
WHEN gs.gs_threshold_type=-11 THEN 'HGNC'
WHEN gs.gs_threshold_type=-12 THEN 'RGD'
WHEN gs.gs_threshold_type=-13 THEN 'ZFIN'
WHEN gs.gs_threshold_type=-14 THEN 'FlyBase'
WHEN gs.gs_threshold_type=-15 THEN 'Wormbase'
WHEN gs.gs_threshold_type=-16 THEN 'SGD'
WHEN gs.gs_threshold_type=-17 THEN 'miRBase'
WHEN gs.gs_threshold_type=-20 THEN 'CGNC'
END AS gene_id_type_name
FROM geneset gs
LEFT OUTER JOIN publication p USING(pub_id)
LEFT OUTER JOIN species sp USING(sp_id)
WHERE gs.gs_status<>'deleted'
), geneset_gene_query AS (
SELECT gs.gs_id, STRING_AGG(ode_ref_id, ' ') AS genes
FROM geneset gs
JOIN geneset_value USING(gs_id)
JOIN gene USING(ode_gene_id)
JOIN gene_info USING(ode_gene_id)
WHERE gs.gs_status <> 'deleted' AND gsv_in_threshold AND ode_pref
GROUP BY gs.gs_id
), geneset_ontology_query AS (
SELECT gso.gs_id, STRING_AGG(o.ont_ref_id || ' ' || o.ont_name || ' ' || o.ont_description, ' ') AS ontologies
FROM ontology o
JOIN geneset_ontology gso ON gso.ont_id = o.ont_id
JOIN geneset gs ON gs.gs_id = gso.gs_id
WHERE gso.gso_ref_type != 'Blacklist' AND gs.gs_status <> 'deleted'
GROUP BY gso.gs_id
)
SELECT gq.gs_id,
gq.usr_id,
gq.gs_count,
gq.pub_id,
gq.pub_pubmed,
gq.taxid,
gq.cur_id,
gq.sp_id,
gq.gs_status,
to_tsvector('english',
COALESCE(gq.gs_id::text, '') || ' ' || COALESCE(gq.gsid_prefixed, '') || ' ' ||
COALESCE(gq.name, '') || ' ' || COALESCE(gq.description, '') || ' ' ||
COALESCE(gq.threshold_name, '') || ' ' || COALESCE(gq.gene_id_type_name, '') || ' ' ||
COALESCE(gq.label, '') || ' ' || COALESCE(gq.pub_id::text, '') || ' ' ||
COALESCE(gq.pub_pubmed, '') || ' ' || COALESCE(gq.pub_authors, '') || ' ' ||
COALESCE(gq.pub_title, '') || ' ' || COALESCE(gq.pub_abstract, '') || ' ' ||
COALESCE(gq.pub_journal, '') || ' ' || COALESCE(gq.species, '') || ' ' ||
COALESCE(gq.taxid::text, '') || ' ' || COALESCE(gq.common_name, '') || ' ' ||
COALESCE(ggq.genes, '') || ' ' || COALESCE(goq.ontologies, '')
) AS _combined_tsvector
FROM geneset_query gq
LEFT JOIN geneset_gene_query ggq ON gq.gs_id = ggq.gs_id
LEFT JOIN geneset_ontology_query goq ON gq.gs_id = goq.gs_id;

CREATE INDEX geneset_search_idx ON production.geneset_search USING gin(_combined_tsvector);

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